Protein-based peptide-bond formation by aminoacyl-tRNA protein transferaseWatanabe, K., Toh, Y., Suto, K., Shimizu, Y., Oka, N., Wada, T., Tomita, K.
(2007) Nature 449: 867-871
- PubMed: 17891155
- DOI: https://doi.org/10.1038/nature06167
- Primary Citation of Related Structures:
2Z3K, 2Z3L, 2Z3M, 2Z3N, 2Z3O, 2Z3P
- PubMed Abstract:
Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.
Institute of Biological Resources and Functions, National Institute of Advanced Industrial Sciences and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.